Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

Church, Deirdre L.; Cerutti, Lorenzo; Gürtler, Antoine; Griener, Thomas P.; Zelazny, Adrian M.; Emler, Stefan

doi:10.1128/cmr.00053-19

Cited by 186 publications

(126 citation statements)

References 586 publications

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“…Proteobacteria and Firmicutes were the dominant phyla, with Escherichia–Shigella, Fusobacterium , and Enterococcus the major genera. Even though the interpretation of 16S sequence data for assigning a definitive bacterial species was limited ( Church et al., 2020 ), E. coli was found to be the most abundant species, which was consistent with traditional culture data. LEfSe revealed that no taxon from the biliary microbiota was found to be differentially more abundant as compared to the duodenal microbiota, suggesting that bile shared similar bacterial communities with duodenal juice in patients with choledocholithiasis.…”

Section: Discussionsupporting

confidence: 70%

Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota

Han

Fan

et al. 2021

Front. Cell. Infect. Microbiol.

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BackgroundThe pathogenesis of choledocholithiasis is closely related to the role of bacteria. However, little is known about the predictive role of bile bacteria in clinical conditions of patients and the compositional and functional characteristics of biliary microbiota in choledocholithiasis.MethodsTo investigate the predictive value of biliary bacteria, clinical data of 488 patients with choledocholithiasis were collected. The predictive value of common bile bacteria to patients’ clinical conditions was analyzed by logistic regression. Samples of bile and corresponding duodenal juice from 10 selected patients with choledocholithiasis were obtained, and the composition and function of microbial communities were analyzed based on 16S rRNA sequencing and Tax4Fun.ResultsThe clinical conditions of patients with choledocholithiasis, such as recurrence, the severity of acute cholangitis, and duration of hospital stay were closely related to different species of bile bacteria as well as antimicrobial-resistant bacteria. Employing 16S rRNA sequencing, the dominant phyla of biliary and duodenal microbiota were Proteobacteria and Firmicutes. The top three core microbiota at the genus level were Escherichia–Shigella, Fusobacterium, and Enterococcus. Escherichia coli accounted for the most abundant annotated species in both. Differences in composition between biliary and duodenal microbiota were not significant according to the alpha and beta diversities. Differential abundant features were not found in biliary microbiota indicated by A linear discriminant analysis effective size algorithm. The major pathways identified in biliary and duodenal microbiota were related to membrane transport, translation, replication and repair, carbohydrate and amino acid metabolism. However, no significant difference in those major pathways, as well as antimicrobial-resistance patterns, was observed between biliary and duodenal microbiota.ConclusionOur study first demonstrates the predictive contribution of biliary bacteria to the clinical conditions of patients with choledocholithiasis, and then it offers new insights into the compositional and functional features of biliary and duodenal microbiota. Similarities between biliary and duodenal microbiota support the theory of bacterial duodenal–biliary reflux in patients with choledocholithiasis. Meanwhile, when it is impracticable to obtain a bile sample, duodenal juice may be used as an alternative for bacterial culture and susceptibility tests.

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Section: Discussionsupporting

confidence: 70%

Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota

Han

Fan

et al. 2021

Front. Cell. Infect. Microbiol.

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“…Nucleic acid sequence of the bacterial 16S rRNA gene has been used for several decades to identify routine identification of bacterial pathogens [18].The 16S rRNA gene sequencing technology was applied to detect the V3-V4 region of bacterial species in twenty-four stool samples from five groups (PBS, CT26, CT26-L, CT26-M, CT26-H) and was entrusted to Personal Bio company.…”

Section: Gm Analysismentioning

confidence: 99%

Effect of Disordered Gut Microbiota on Serum Metabolome Alterations in Colorectal Tumor-Bearing Mice Under The Intervention of Fufangchangtai

Cai

Lin

Xiao

et al. 2021

Preprint

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Background: The occurrence and development of colorectal cancer is related to the compositional and functional variation of gut microbiota. Compared with healthy people, gut microbiota of patients with colorectal cancer is in disorder. Most traditional Chinese Medicine is effective by oral administration and has both anti-tumor effect and enteric microecological regulative effect. However, whether the dysbiosis of gut microbiota under tumor burden affects the serum metabolome of human body that related to traditional Chinese medicine is unclear. In this study, Fufangchangtai (FFCT) was chosen to be the model prescription to explore the correlation between gut microbiota and the serum metabolism related to FFCT in anti colorectal cancer treatment. Results: The gut microbiota between colorectal tumor-bearing mice and healthy mice were determined by 16S rRNA gene sequencing, showing quite differences between the two groups and suggesting that Firmicutes , Deferribacteres , Bacteroidetes and Proteobacteria were marked differential intestinal bacteria. The alternations in serum metabolome in the FFCT-treating tumor-bearing mice and simple FFCT-treating mice were detected using Liquid chromatogragh-mass spectrometer (LC/MS), showing significant differences between the two groups as well. Metabolites of FFCT like Citric acid, （±）12-HEPE, Cycloartanyl ferulate were much more in simple FFCT-treating mice, indicating that the present of tumor could affect the absorption and metabolism of FFCT. Additionally, these differential metabolites of FFCT involved in multiple pathways including the Alanine, aspartate and glutamate metabolism, Central carbon metabolism in cancer, Biosynthesis of amino acids. Different doses of FFCT were given to the tumor-bearing mice through oral administration, and the results of gut microbiota 16S rRNA gene sequencing showing that FFCT-treating groups has higher abundance of Firmicutes , Turicibacter and Roseburia than tumor-bearing group, moreover, the abundance of these bacteria was positively correlated to the drug concentration. Firmicutes and Bacteroidetes in FFCT-treating groups showed a similar trend with Healthy group, indicating the modulation of FFCT on gut microbiota of colorectal tumor-bearing mice.Conclusions: Collectively, we concluded that the dysbiosis of gut microbiota in tumor-bearing mice could affect the serum metabolome of human body that related to FFCT, and FFCT could correct the gut microbiota of colorectal tumor-bearing mice. It was pointed out that the GM should be concerned during the therapy of FFCT. The more healthier intestinal microenvironment was conductive to the better clinical curative effect.

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“…Of note, Sabat et al reported improved bacterial species identification via targeted NGS of both 16S and 23S rRNA sequences [43], where the sequencing was performed on DNA extracted directly from urine and orthopedic samples, in addition to those from blood culture bottles. A recent review by Church et al provides a comprehensive summary on the performance of the 16S rRNA gene sequence for bacterial identification [90].…”

Section: Low Taxonomical Resolution In 16sngs Sequencing Readsmentioning

confidence: 99%

Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

et al. 2020

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Bacterial culture and biochemical testing (CBtest) have been the cornerstone of pathogen identification in the diagnostic microbiology laboratory. With the advent of Sanger sequencing and later, next-generation sequencing, 16S rRNA next-generation sequencing (16SNGS) has been proposed to be a plausible platform for this purpose. Nevertheless, usage of the 16SNGS platform has both advantages and limitations. In addition, transition from the traditional methods of CBtest to 16SNGS requires procurement of costly equipment, timely and sustainable maintenance of these platforms, specific facility infrastructure and technical expertise. All these factors pose a challenge for middle-income countries, more so for countries in the lower middle-income range. In this review, we describe the basis for CBtest and 16SNGS, and discuss the limitations, challenges, advantages and future potential of using 16SNGS for bacterial pathogen identification in diagnostic microbiology laboratories of middle-income countries.

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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory

Cited by 186 publications

References 586 publications

Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota

Biliary Microbiota in Choledocholithiasis and Correlation With Duodenal Microbiota

Effect of Disordered Gut Microbiota on Serum Metabolome Alterations in Colorectal Tumor-Bearing Mice Under The Intervention of Fufangchangtai

Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

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